Estimating Database
This menu allows the user to access the phyconst.mdb data base to modify or add to the calculation/interpolation data used by Sednterp. The two things most likely to be modified by users are additions of conjugates and/or unusual amino acids. If adding amino acids it is important to note that each must be given unique 3-letter and 1-letter abbreviations (fields called "namethree" and "nameone"), and that no distinction is made between upper and lower case alphabetic characters. In addition to the obvious molecular weight and vbar fields, each of these records contains entries labeled "hiph7" and "hiph4" that contain the hydration at neutral and low pH in moles of water per mole of the compound. The "covalent" field for amino acids should always be set to 1. The "covalent" field for conjugates should be set to 1 if this is a true covalent conjugate and zero if this is a "loosely bound conjugate" that merely alters the effective vbar of the parent compound, but which is not counted in calculating the molecular weight. The "extinction" entry is not presently used. For charged compounds the "charge" entry should be non-zero and the corresponding "pKa" value should be entered. The "carbo" field should be set to 1 for carbohydrates; this entry is used in calculating vbar for glycoproteins denatured in 6M guanidine HCl (see Calculating Denatured v-bar Estimates). Lastly, for conjugates the "Mcutoff" field is used for "loosely bound conjugates" to indicate the highest molarity for which the vbar entry applies.
The extinction entries in the database are used both in calculating the absorbance properties at 280 nm reported on the Sample Composition Form, and in displaying graphs of the calculated absorbance properties over the 250-320 nm range (see Graphs Available). As supplied, the only compounds with defined extinction spectra are phenylalanine, tyrosine, tryptophan, and disulfide (cistine). You may add data for other conjugates if you like (and certainly there are conjugates already in the database which have significant absorbance in this region, but appropriate extinction data for these was not available to the authors). If you are adding new data, please note that you must enter values for each 2 nm interval from 250-320 nm (this range is fixed in the program), and that the name must exactly match the name defined for the conjugate in the conjugate section of the database (or the 3-letter name for an amino acid). Also, if you have such data, please share it with the authors so it can be provided to all users.
Great caution should be used in modifying the density and viscosity coefficients and the properties of the common amino acids, since the computations performed by Sednterp depend upon this information, yet this information is not easily noted by the user. If this data base is modified, two different versions of Sednterp (or one version at a later date) will give divergent estimates for buffer density or viscosity, and thereby will give different final results for the exact same data entry.
If you have questions regarding how to add to or modify entries in this database, please contact the programmers. Moreover, if you believe you have found errors in this database that you wish to correct in your own copy, the programmers ask that you please contact us so that we may publish the fixes to all interested parties.
The assumptions used in the databases are covered above in the theory section. See the Table of Contents section II, D.
